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- PDB-2v2e: Structure of isoniazid (INH) bound to cytochrome c peroxidase mut... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v2e | ||||||
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Title | Structure of isoniazid (INH) bound to cytochrome c peroxidase mutant N184R Y36A | ||||||
![]() | CYTOCHROME C PEROXIDASE | ||||||
![]() | OXIDOREDUCTASE / CYTOCHROME C PEROXIDASE / TRANSIT PEPTIDE / ORGANIC RADICAL / HYDROGEN PEROXIDE / INH / CCP / IRON / HEME / ISONIAZID / PEROXIDASE / MITOCHONDRION / METAL-BINDING | ||||||
Function / homology | ![]() cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / peroxidase activity / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Metcalfe, C.L. / Macdonald, I.K. / Brown, K.A. / Raven, E.L. / Moody, P.C.E. | ||||||
![]() | ![]() Title: The Tuberculosis Prodrug Isoniazid Bound to Activating Peroxidases. Authors: Metcalfe, C.L. / Macdonald, I.K. / Murphy, E.J. / Brown, K.A. / Raven, E.L. / Moody, P.C.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.2 KB | Display | ![]() |
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PDB format | ![]() | 110.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 799.3 KB | Display | ![]() |
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Full document | ![]() | 800.8 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2v23SC ![]() 2vcfC ![]() 2vcnC ![]() 2vcsC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33583.406 Da / Num. of mol.: 1 / Fragment: RESIDUES 71-361 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PT7CCP/Y39A/N184R / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-ISZ / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.84 % / Description: NONE |
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Crystal grow | Method: microdialysis / pH: 6 Details: MICRODIALYSIS INTO 50MM POTASSIUM PHOSPHATE, PH 6.0 CONTAINING 30% V/V MPD. ISONIAZID WAS DISSOLVED INTO THE MOTHER LIQUOR (300MM) AND SOAKED INTO THE CRYSTAL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: XENOCS MULTI-LAYER |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→30.28 Å / Num. obs: 38990 / % possible obs: 81.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.68→1.77 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5.8 / % possible all: 20.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2V23 Resolution: 1.68→30.28 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.047 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→30.28 Å
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Refine LS restraints |
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